BioC experimental data: CHECK report for yriMulti on malbec2

##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings yriMulti_0.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/yriMulti.Rcheck’
* using R version 3.4.2 (2017年09月28日)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘yriMulti/DESCRIPTION’ ... OK
* this is package ‘yriMulti’ version ‘0.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
 ‘gQTLBase’ ‘SummarizedExperiment’ ‘GenomicRanges’ ‘Homo.sapiens’
 ‘dsQTL’ ‘geuvPack’ ‘MultiAssayExperiment’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘yriMulti’ can be installed ... OK
* checking installed package size ... NOTE
 installed size is 179.5Mb
 sub-directories of 1Mb or more:
 data 179.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘MultiAssayExperiment’
 These packages need to be imported from (in the NAMESPACE file)
 for when this namespace is loaded but not attached.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
checkGenomes: no visible global function definition for ‘genome’
mexGR: no visible global function definition for ‘subjectHits’
mexGR : embell: no visible global function definition for ‘DataFrame’
mexGR: no visible global function definition for ‘IRanges’
mexGR: no visible global function definition for ‘new’
plotEvM: no visible global function definition for ‘metadata’
pwplot: no visible global function definition for ‘experiments’
show,mexGR: no visible global function definition for ‘selectSome’
Undefined global functions or variables:
 DataFrame IRanges experiments genome metadata new selectSome
 subjectHits
Consider adding
 importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... WARNING
prepare_Rd: mexGR.Rd:34-36: Dropping empty section \details
prepare_Rd: mexGR.Rd:51-53: Dropping empty section \note
prepare_Rd: mexGR.Rd:48-50: Dropping empty section \author
prepare_Rd: mexGR.Rd:45-47: Dropping empty section \references
prepare_Rd: mexGR.Rd:57-59: Dropping empty section \seealso
prepare_Rd: pwplot.Rd:7-9: Dropping empty section \description
prepare_Rd: pwplot.Rd:40-42: Dropping empty section \details
checkRd: (5) pwplot.Rd:0-70: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
 ‘demoMAE’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
 
 Note: significantly better compression could be obtained
 by using R CMD build --resave-data
 old_size new_size compress
 banovichSE.rda 172.2Mb 114.9Mb xz
 demoMAE.rda 6.8Mb 5.9Mb xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
 user system elapsed
mexGR 12.304 0.176 12.492
banovichSE 6.112 0.060 6.174
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
 ‘GenomeInfoDb’ ‘GenomicFiles’ ‘VariantAnnotation’ ‘bibtex’
 ‘doParallel’ ‘gQTLstats’ ‘knitcitations’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 6 NOTEs
See
 ‘/home/biocbuild/bbs-3.5-data-experiment/meat/yriMulti.Rcheck/00check.log’
for details.

* installing *source* package ‘yriMulti’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (yriMulti)